1-(4,6-Dimethyl­pyrimidin-2-yl)thio­urea

Saeed, S.; Rashid, N.; Jasinski, J.P.; Golen, J.A.

doi:10.1107/S1600536811048148

organic compounds

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ISSN: 2056-9890

Volume 67| Part 12| December 2011| Page o3347

https://doi.org/10.1107/S1600536811048148

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1-(4,6-Dimethylpyrimidin-2-yl)thiourea

Sohail Saeed,^a ^* Naghmana Rashid,^a Jerry P. Jasinski ^b and James A. Golen ^b

^aDepartment of Chemistry, Research Complex, Allama Iqbal Open University, Islamabad 44000, Pakistan, and ^bDepartment of Chemistry, Keene State College, 229 Main Street, Keene, NH 03435-2001, USA
^*Correspondence e-mail: sohail262001@yahoo.com

(Received 23 October 2011; accepted 13 November 2011; online 19 November 2011)

In the crystal structure of the title compound, C₇H₁₀N₄S, weak intermolecular N—H⋯S interactions form a two-dimensional network parallel to the ab plane. An intramolecular N—H⋯N hydrogen bond occurs.

Related literature

For structural characterization of N-substituted thiourea derivatives with heterocyclic substituents, see: Saeed et al. (2010a ,b , 2011 ). For standard bond lengths, see Allen et al. (1987 ).

Experimental

Crystal data

C₇H₁₀N₄S
M_r = 182.25
Orthorhombic, P n a 2₁
a = 8.3372 (5) Å
b = 15.8303 (10) Å
c = 6.618 (1) Å
V = 873.45 (15) Å³
Z = 4
Mo Kα radiation
μ = 0.32 mm⁻¹
T = 173 K
0.30 × 0.20 × 0.18 mm

Data collection

Oxford DiffractionXcalibur Eos Gemini diffractometer
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2010 $[Oxford Diffraction (2010). CrysAlis PRO and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]$ ) T_min = 0.910, T_max = 0.945
7240 measured reflections
2057 independent reflections
1588 reflections with I > 2σ(I)
R_int = 0.043

Refinement

R[F² > 2σ(F²)] = 0.053
wR(F²) = 0.144
S = 1.10
2057 reflections
120 parameters
4 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.57 e Å⁻³
Δρ_min = −0.23 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯N4	0.90 (2)	1.99 (3)	2.676 (3)	131 (3)
N1—H1B⋯S1ⁱ	0.87 (2)	2.58 (2)	3.399 (2)	159 (4)
N2—H2A⋯S1ⁱⁱ	0.85 (2)	2.53 (2)	3.338 (2)	160 (4)
Symmetry codes: (i) $[x-{\script{1\over 2}}, -y+{\script{3\over 2}}, z]$ ; (ii) $[x+{\script{1\over 2}}, -y+{\script{3\over 2}}, z]$ .

Data collection: CrysAlis PRO (Oxford Diffraction, 2010 $[Oxford Diffraction (2010). CrysAlis PRO and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]$ ); cell refinement: CrysAlis PRO; data reduction: CrysAlis RED (Oxford Diffraction, 2010 $[Oxford Diffraction (2010). CrysAlis PRO and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]$ ); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536811048148/im2335sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536811048148/im2335Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S1600536811048148/im2335Isup3.cml

checkCIF report

Comment top

The crystal structure of the title compound is a byproduct of the reaction of 1-(4,6-dimethylpyrimidin-2-yl)-3-(3,5-dinitrophenyl)thiourea with a copper acetate salt. It is related to our previous studies on the structural chemistry of heterocyclic compounds containing an N-substituted thiourea (Saeed et al., 2010a, 2010b, 2011). Herein, as a continuation of these studies, the structure of the title compound, (I), C₇H₁₀N₄S, is described.

In the title compound, (I), (Fig. 1) the crystal packing is realized by intramolecular N1—H1···N4 hydrogen bonds and weak N—H···S intermolecular interactions (Table 1) forming a 2-D network along [110] (Fig. 2). Bond distances are in normal ranges (Allen et al. (1987).

Related literature top

For structural characterization of N-substituted thiourea derivatives with heterocyclic substituents, see: Saeed et al. (2010a,b, 2011). For standard bond lengths, see Allen et al. (1987).

Experimental top

After refluxing a reaction mixture of 1-(4,6-dimethylpyrimidin-2-yl)-3- (3,5-dinitrophenyl)thiourea with copper acetate salt, it was transfered into cold water. The crude solid product was filtered, washed again with water and purified by re-crystallization from ethanol (Yield: 45%). Single crystals of the title compound were obtained by recrystallisation from a dichloromethane/ethanol mixture (2:1).

Structure description top

For structural characterization of N-substituted thiourea derivatives with heterocyclic substituents, see: Saeed et al. (2010a,b, 2011). For standard bond lengths, see Allen et al. (1987).

Computing details top

Data collection: CrysAlis PRO (Oxford Diffraction, 2010); cell refinement: CrysAlis PRO (Oxford Diffraction, 2010); data reduction: CrysAlis RED (Oxford Diffraction, 2010); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. Molecular structure of the title compound showing the atom labeling scheme and 30% probability displacement ellipsoids.
	Fig. 2. Packing diagram of the title compound viewed along the c axis. Dashed lines indicate weak N—H···S intermolecular interactions forming a 2-D network along [110].

1-(4,6-Dimethylpyrimidin-2-yl)thiourea top

Crystal data top

C₇H₁₀N₄S	F(000) = 384
M_r = 182.25	D_x = 1.386 Mg m⁻³
Orthorhombic, Pna2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2n	Cell parameters from 2136 reflections
a = 8.3372 (5) Å	θ = 3.3–32.5°
b = 15.8303 (10) Å	µ = 0.32 mm⁻¹
c = 6.618 (1) Å	T = 173 K
V = 873.45 (15) Å³	Block, pale yellow
Z = 4	0.30 × 0.20 × 0.18 mm

Data collection top

Oxford DiffractionXcalibur Eos Gemini diffractometer	2057 independent reflections
Radiation source: Enhance (Mo) X-ray Source	1588 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.043
Detector resolution: 16.1500 pixels mm^-1	θ_max = 27.9°, θ_min = 3.3°
ω scans	h = −10→10
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2010)	k = −20→20
T_min = 0.910, T_max = 0.945	l = −8→8
7240 measured reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.053	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.144	H atoms treated by a mixture of independent and constrained refinement
S = 1.10	w = 1/[σ²(F_o²) + (0.0705P)² + 0.3395P] where P = (F_o² + 2F_c²)/3
2057 reflections	(Δ/σ)_max = 0.021
120 parameters	Δρ_max = 0.57 e Å⁻³
4 restraints	Δρ_min = −0.23 e Å⁻³

Crystal data top

C₇H₁₀N₄S	V = 873.45 (15) Å³
M_r = 182.25	Z = 4
Orthorhombic, Pna2₁	Mo Kα radiation
a = 8.3372 (5) Å	µ = 0.32 mm⁻¹
b = 15.8303 (10) Å	T = 173 K
c = 6.618 (1) Å	0.30 × 0.20 × 0.18 mm

Data collection top

Oxford DiffractionXcalibur Eos Gemini diffractometer	2057 independent reflections
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2010)	1588 reflections with I > 2σ(I)
T_min = 0.910, T_max = 0.945	R_int = 0.043
7240 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.053	4 restraints
wR(F²) = 0.144	H atoms treated by a mixture of independent and constrained refinement
S = 1.10	Δρ_max = 0.57 e Å⁻³
2057 reflections	Δρ_min = −0.23 e Å⁻³
120 parameters

Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
S1	0.39504 (8)	0.77736 (4)	0.3627 (3)	0.0334 (2)
N1	0.2593 (2)	0.62628 (14)	0.3662 (11)	0.0295 (5)
H1A	0.261 (4)	0.5693 (11)	0.374 (13)	0.035*
H1B	0.179 (3)	0.6589 (17)	0.338 (8)	0.035*
N2	0.5367 (2)	0.62855 (12)	0.3683 (10)	0.0241 (5)
H2A	0.615 (3)	0.6613 (16)	0.345 (9)	0.029*
N3	0.7243 (2)	0.52446 (13)	0.3633 (9)	0.0309 (6)
N4	0.4441 (3)	0.48807 (14)	0.3725 (8)	0.0263 (5)
C1	0.3948 (3)	0.67031 (15)	0.3601 (11)	0.0246 (6)
C2	0.5672 (3)	0.54221 (16)	0.3715 (9)	0.0265 (6)
C3	0.7616 (3)	0.44226 (17)	0.3597 (12)	0.0310 (6)
C4	0.6435 (3)	0.38055 (16)	0.3665 (14)	0.0318 (6)
H4A	0.6711	0.3225	0.3786	0.038*
C5	0.4852 (3)	0.40536 (17)	0.3554 (10)	0.0292 (7)
C6	0.3496 (3)	0.34350 (17)	0.3676 (15)	0.0403 (8)
H6A	0.2609	0.3629	0.2823	0.060*
H6B	0.3130	0.3390	0.5079	0.060*
H6C	0.3863	0.2881	0.3205	0.060*
C7	0.9355 (3)	0.42072 (19)	0.3708 (14)	0.0413 (9)
H7A	0.9991	0.4684	0.3206	0.062*
H7B	0.9568	0.3707	0.2878	0.062*
H7C	0.9648	0.4089	0.5114	0.062*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0193 (3)	0.0239 (3)	0.0570 (5)	0.0017 (2)	−0.0110 (6)	−0.0034 (11)
N1	0.0161 (10)	0.0256 (10)	0.0466 (15)	0.0014 (8)	−0.007 (3)	−0.008 (3)
N2	0.0173 (10)	0.0222 (10)	0.0328 (13)	−0.0013 (8)	−0.005 (3)	−0.005 (3)
N3	0.0206 (11)	0.0298 (12)	0.0424 (16)	0.0013 (8)	−0.015 (2)	−0.008 (3)
N4	0.0254 (11)	0.0278 (10)	0.0257 (14)	−0.0015 (8)	−0.006 (2)	0.003 (2)
C1	0.0197 (11)	0.0293 (12)	0.0248 (15)	0.0002 (9)	−0.012 (2)	−0.001 (3)
C2	0.0257 (13)	0.0284 (12)	0.0254 (16)	−0.0001 (9)	−0.008 (3)	0.003 (3)
C3	0.0247 (13)	0.0335 (14)	0.0347 (17)	0.0019 (10)	−0.009 (3)	−0.006 (3)
C4	0.0270 (13)	0.0255 (12)	0.0430 (17)	0.0021 (10)	0.007 (4)	0.007 (4)
C5	0.0258 (13)	0.0304 (13)	0.0315 (18)	−0.0027 (10)	−0.009 (2)	0.003 (3)
C6	0.0283 (14)	0.0319 (14)	0.061 (2)	−0.0073 (11)	−0.013 (4)	0.001 (5)
C7	0.0291 (14)	0.0356 (15)	0.059 (2)	0.0061 (12)	−0.014 (4)	−0.001 (4)

Geometric parameters (Å, º) top

S1—C1	1.695 (3)	C3—C4	1.388 (4)
N1—C1	1.328 (3)	C3—C7	1.491 (4)
N1—H1A	0.904 (17)	C4—C5	1.379 (4)
N1—H1B	0.869 (18)	C4—H4A	0.9500
N2—C1	1.356 (3)	C5—C6	1.497 (4)
N2—C2	1.390 (3)	C6—H6A	0.9800
N2—H2A	0.846 (17)	C6—H6B	0.9800
N3—C3	1.338 (3)	C6—H6C	0.9800
N3—C2	1.341 (3)	C7—H7A	0.9800
N4—C2	1.337 (3)	C7—H7B	0.9800
N4—C5	1.358 (3)	C7—H7C	0.9800

C1—N1—H1A	120.7 (19)	C5—C4—H4A	120.8
C1—N1—H1B	110 (2)	C3—C4—H4A	120.8
H1A—N1—H1B	128 (3)	N4—C5—C4	120.8 (3)
C1—N2—C2	129.7 (2)	N4—C5—C6	115.8 (3)
C1—N2—H2A	112 (2)	C4—C5—C6	122.2 (2)
C2—N2—H2A	118 (2)	C5—C6—H6A	109.5
C3—N3—C2	115.6 (2)	C5—C6—H6B	109.5
C2—N4—C5	115.1 (2)	H6A—C6—H6B	109.5
N1—C1—N2	119.0 (2)	C5—C6—H6C	109.5
N1—C1—S1	121.71 (19)	H6A—C6—H6C	109.5
N2—C1—S1	119.07 (17)	H6B—C6—H6C	109.5
N4—C2—N3	128.0 (2)	C3—C7—H7A	109.5
N4—C2—N2	119.3 (2)	C3—C7—H7B	109.5
N3—C2—N2	112.6 (2)	H7A—C7—H7B	109.5
N3—C3—C4	121.2 (2)	C3—C7—H7C	109.5
N3—C3—C7	116.6 (2)	H7A—C7—H7C	109.5
C4—C3—C7	121.8 (2)	H7B—C7—H7C	109.5
C5—C4—C3	118.5 (2)

C2—N2—C1—N1	4.0 (12)	C2—N3—C3—C4	−0.7 (11)
C2—N2—C1—S1	178.8 (6)	C2—N3—C3—C7	−174.2 (6)
C5—N4—C2—N3	−2.7 (10)	N3—C3—C4—C5	6.9 (12)
C5—N4—C2—N2	173.7 (5)	C7—C3—C4—C5	180.0 (8)
C3—N3—C2—N4	−1.4 (10)	C2—N4—C5—C4	9.0 (11)
C3—N3—C2—N2	−178.1 (6)	C2—N4—C5—C6	176.8 (6)
C1—N2—C2—N4	−2.1 (11)	C3—C4—C5—N4	−11.2 (12)
C1—N2—C2—N3	174.9 (8)	C3—C4—C5—C6	−178.2 (8)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···N4	0.90 (2)	1.99 (3)	2.676 (3)	131 (3)
N1—H1B···S1ⁱ	0.87 (2)	2.58 (2)	3.399 (2)	159 (4)
N2—H2A···S1ⁱⁱ	0.85 (2)	2.53 (2)	3.338 (2)	160 (4)

Symmetry codes: (i) x−1/2, −y+3/2, z; (ii) x+1/2, −y+3/2, z.

Experimental details

Crystal data
Chemical formula	C₇H₁₀N₄S
M_r	182.25
Crystal system, space group	Orthorhombic, Pna2₁
Temperature (K)	173
a, b, c (Å)	8.3372 (5), 15.8303 (10), 6.618 (1)
V (Å³)	873.45 (15)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.32
Crystal size (mm)	0.30 × 0.20 × 0.18

Data collection
Diffractometer	Oxford DiffractionXcalibur Eos Gemini
Absorption correction	Multi-scan (CrysAlis RED; Oxford Diffraction, 2010)
T_min, T_max	0.910, 0.945
No. of measured, independent and observed [I > 2σ(I)] reflections	7240, 2057, 1588
R_int	0.043
(sin θ/λ)_max (Å⁻¹)	0.658

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.053, 0.144, 1.10
No. of reflections	2057
No. of parameters	120
No. of restraints	4
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.57, −0.23

Computer programs: CrysAlis PRO (Oxford Diffraction, 2010), CrysAlis RED (Oxford Diffraction, 2010), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···N4	0.904 (17)	1.99 (3)	2.676 (3)	131 (3)
N1—H1B···S1ⁱ	0.869 (18)	2.58 (2)	3.399 (2)	159 (4)
N2—H2A···S1ⁱⁱ	0.846 (17)	2.53 (2)	3.338 (2)	160 (4)

Symmetry codes: (i) x−1/2, −y+3/2, z; (ii) x+1/2, −y+3/2, z.

Acknowledgements

JPJ acknowledges the NSF–MRI program (grant No. CHE1039027) for funds to purchase the X-ray diffractometer.

References

Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19. CSD CrossRef Web of Science Google Scholar
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